Import command

[will-moore]

What do we call this command?

Please indicate your preferred name for the command. We will obviously need to add documentation

• Will - import
• JM: - record
• Petr: - record
• Dom: import
• Jason: 'import'
• Josh: "No objections [to import]"

---

This takes the register.py script from BioNGFF/omero-import-utils#24 and adds it to omero-cli-zarr.

This still gives us nice features:

• We can run omero zarr import ... from anywhere (don't have to cd to omero-import-utils/metadata)
• integration tests are added to test the import of most images from Testing data for registration BioNGFF/omero-import-utils#13
• pip installable
• mypy checking etc

To test:

• look at integration tests. They are testing both the command line and the usage of register_zarr(url) method.
• checkout this branch, $ cd omero-cli-zarr and then $ pip install -e .
• Use examples at Testing data for registration BioNGFF/omero-import-utils#13 to test, e.g

$ omero zarr register --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr

[will-moore]

This looks like similar issues to those discussed at #172 (comment) (also still failing checks there)...

"The jobs above are failing on the mypy check being run by omero-test-infra, so that's where we need to fix the python version.

How do I find out the version of python used by omero-test-infra, and can I control it?

The issue of python-version for omero-test-infra was also asked about at ome/omero-web-zarr#19 (comment)

cc @joshmoore

[will-moore]

Checks above are failing, but test is running and passing locally:

(omeroweb2) M-002366:omero-cli-zarr wmoore$ cd test/
(omeroweb2) M-002366:test wmoore$ pytest integration/clitest/test_register.py 
============================ test session starts ============================
platform darwin -- Python 3.9.15, pytest-7.3.1, pluggy-1.0.0
rootdir: /Users/wmoore/Desktop/ZARR/omero-cli-zarr
plugins: hypothesis-6.100.1, dash-2.9.3, napari-0.4.17, napari-plugin-engine-0.2.0, django-4.8.0, anyio-4.2.0
collected 6 items                                                                                                                                    

integration/clitest/test_register.py ......                                                        [100%]

============= warnings summary =========================
../../../../opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/Ice.py:14
  /Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/Ice.py:14: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
    import sys, string, imp, os, threading, warnings, datetime

../../../../opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/skimage/util/dtype.py:27
  /Users/wmoore/opt/anaconda3/envs/omeroweb2/lib/python3.9/site-packages/skimage/util/dtype.py:27: DeprecationWarning: `np.bool8` is a deprecated alias for `np.bool_`.  (Deprecated NumPy 1.24)
    np.bool8: (False, True),

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
================== 6 passed, 2 warnings in 28.30s =========================

[will-moore]

Build errors seem to be due to Zarr v3 references:

src/omero_zarr/register.py:88: error: Name "zarr.core.Array" is not defined  [name-defined]
src/omero_zarr/register.py:89: error: Module has no attribute "open"  [attr-defined]
src/omero_zarr/register.py:97: error: Module has no attribute "open"  [attr-defined]
src/omero_zarr/register.py:633: error: Module has no attribute "errors"  [attr-defined]

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-plugins-push#516. See the console output for more details.
Possible conflicts:

• PR Use zarr v3 and updated ome-zarr-py #172 will-moore 'Use zarr v3 and updated ome-zarr-py'
  • .github/workflows/omero_plugin.yml

--conflicts Conflict resolved in build OMERO-plugins-push#517. See the console output for more details.

[dominikl]

Looks good to me! Thanks Will. I guess before mergeing we have to discuss/decide on the name import/register/??? .

[dominikl]

Actually, just noticed that this doesn't seem to work with local files on the file system:

> omero zarr register --target 3751 /data/testing/sarscov2-phenomics-repurposing/bioformats-convert-PP103554
...
  File "/home/dlindner/micromamba/envs/import/lib/python3.12/site-packages/omero_zarr/register.py", line 639, in register_zarr
    store = zarr.storage.LocalStore(uri, read_only=True)
            ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'LocalStore'

[will-moore]

@dominikl I think that looks like you have zarr v3 in your local env. You need zarr v2

[dominikl]

Indeed. There's something odd going on. I simply checkout this branch and pip install . This will install zarr-2.18.7. Then pip install -U zarr will install zarr 3 but uninstall omero-cli-zarr. Then installing omero-cli-zarr again, will remove zarr 3 and install zarr 2 again. Doesn't seem to be possible to have both!?

[dominikl]

Sorry, installing zarr 3 does not uninstall omero-cli-zarr, it just break it:

  File "/home/dlindner/micromamba/envs/import/lib/python3.12/site-packages/ome_zarr/format.py", line 7, in <module>
    from zarr.storage import FSStore
ImportError: cannot import name 'FSStore' from 'zarr.storage'

[will-moore]

DON'T INSTALL ZARR V3.
YOU NEED ZARR V2.

[dominikl]

> git log
commit b8c63a5b03b25b3a39748b27729f50d97a5385de (HEAD, will/register_command)
Author: William Moore <[email protected]>
Date:   Thu Aug 28 16:38:32 2025 +0100

    don't use delete_on_close for tempfile (py312 only)

> pip install .
...
Successfully installed aiobotocore-2.24.2 aiohappyeyeballs-2.6.1 aiohttp-3.12.15 aioitertools-0.12.0 aiosignal-1.4.0 asciitree-0.3.3 attrs-25.3.0 botocore-1.40.18 click-8.2.1 cloudpickle-3.1.1 dask-2025.7.0 deprecated-1.2.18 fasteners-0.20 frozenlist-1.7.0 fsspec-2025.9.0 imageio-2.37.0 jmespath-1.0.1 lazy-loader-0.4 locket-1.0.0 multidict-6.6.4 networkx-3.5 numcodecs-0.15.1 ome-zarr-0.11.1 omero-cli-zarr-0.5.6.dev72+gb8c63a5 partd-1.4.2 propcache-0.3.2 s3fs-2025.9.0 scikit-image-0.25.2 scipy-1.16.1 tifffile-2025.8.28 toolz-1.0.0 typing-extensions-4.15.0 wrapt-1.17.3 yarl-1.20.1 zarr-2.18.7

> pip freeze
zarr==2.18.7

> omero zarr register --target 3751 /data/testing/sarscov2-phenomics-repurposing/bioformats-convert-PP103554
Using session for demo@localhost:4064. Idle timeout: 10 min. Current group: Public
Registering zarr file as an Image in OMERO /data/testing/sarscov2-phenomics-repurposing/bioformats-convert-PP103554
Traceback (most recent call last):
...
  File "/home/dlindner/micromamba/envs/import_2/lib/python3.12/site-packages/omero_zarr/register.py", line 639, in register_zarr
    store = zarr.storage.LocalStore(uri, read_only=True)
            ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'zarr.storage' has no attribute 'LocalStore'

[will-moore]

Sorry, my bad. It is a case of zarr 3 vv 2 mixup, and you do need zarr v2, but that line is wrong.

Try

store = zarr.storage.NestedDirectoryStore(uri)

[dominikl]

Thanks Will, that fixes the problem!

[will-moore]

@dominikl I added that fix, and also ported the labels code from https://github.com/BioNGFF/omero-import-utils/pull/7/files.

Tested with:

$ omero zarr register https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr --target 22521 --labels

[jburel]

I understood that we were not going to include labels for now as part of this workflow

[will-moore]

@jburel I understood that we were going to prioritise the migration from BioNGFF/omero-import-utils to here ahead of merging the labels PR there (which we've done).
But the labels functionality is useful (Dom was using it for IDR and was asking about it) so it makes sense to bring it along too. It's still under an optional flag, so doesn't change the default behaviour (NB: I still need to find some suitable Plates and bioformats2raw samples with labels to test those).

[jburel]

@jburel I understood that we were going to prioritise the migration from BioNGFF/omero-import-utils to here ahead of merging the labels PR there (which we've done). But the labels functionality is useful (Dom was using it for IDR and was asking about it) so it makes sense to bring it along too. It's still under an optional flag, so doesn't change the default behaviour (NB: I still need to find some suitable Plates and bioformats2raw samples with labels to test those).

BioNGFF/omero-import-utils#7 The PR was closed. We decided not to merge it due to the time it was taking, we have to read the binary data when supporting labels. I understand that it can be useful but I think we need more tests before pushing forward with that option
I believe the files are local in @dominikl case.
Labels support should be investigated as a follow-up

[will-moore]

The PR was only closed after copying it over to this PR.

I just uploaded a new sample that is bioformats2raw layout containing 3 images, 2 of which have labels.

Imported into merge-ci...

$ omero zarr import https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr --labels --target 23619

I could revert that and move it to another branch, on top of this one, but it might be nicer to just do a bit more testing on this one? @dominikl

[jburel]

I don't think it was solely closed because we started working on this repository.
We discussed not involving the reading of the binary due to potential performance issues

My preference:

• Create a release candidate with support for images and not labels. I will also disable plate support for now
• Look at asynchronous support for plate and labels as follow up works

[dominikl]

Thanks, looks good to me. Tested with some examples from BioNGFF/omero-import-utils#13. Also no --labels option any longer, and trying to import plate says that it's not supported yet. 👍
Hopefully you can easily revert your last two commits and open separate PRs for them (I think there's a git command for it?).

[jburel]

suggestion: 0.7.0rc1

[will-moore]

@dominikl I just pushed a couple of commits to update the README, to add import info, and also to update a VERY old like to the spec! Staged at https://github.com/will-moore/omero-cli-zarr/tree/register_command

[dominikl]

👍 Thanks, looks good to me!